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Related Concept Videos

Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

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Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...

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Updated: Jun 9, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Towards site-based protein functional annotations.

Seak Fei Lei1, Jun Huan

  • 1School of Electrical Engineering and Computer Science, University of Kansas, Lawrence, Kansas 66045, USA. slei@eecs.ku.edu

International Journal of Data Mining and Bioinformatics
|September 7, 2010
PubMed
Summary
This summary is machine-generated.

We developed novel methods to predict protein function using local structures. These approaches improve functional annotation accuracy by reducing random matches in protein active sites.

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Last Updated: Jun 9, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
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Published on: November 3, 2011

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein function prediction

Background:

  • The precise link between protein active sites and their functions remains elusive despite extensive research.
  • Accurate protein function prediction is crucial for understanding biological processes and drug discovery.

Purpose of the Study:

  • To enhance protein function prediction accuracy by leveraging local structural information.
  • To develop and validate novel computational methods for identifying functionally relevant protein regions.

Main Methods:

  • Utilized Markov Random Fields (MRF) to model protein active regions.
  • Implemented a filtering approach incorporating the local environment of active sites.
  • Generated multiple structure motifs by expanding motifs to adjacent residues.

Main Results:

  • Experimental validation on enzyme families with less than 40% sequence identity.
  • Demonstrated a significant reduction in random matches compared to traditional methods.
  • Achieved up to a 70% improvement in functional annotation ability, measured by area under the curve.

Conclusions:

  • The proposed methods effectively utilize local structural features for improved protein function prediction.
  • These computational strategies offer a robust approach to overcoming limitations in current functional annotation techniques.
  • The findings contribute to a better understanding of structure-function relationships in proteins.